siRNA vs shRNA

siRNA or shRNA?

Whilst there are several options for synthetic and expressed RNAi: the most commonly-used form of synthetic RNAi is siRNA, and of expressed RNAi is shRNA. Benitec's ddRNAi patents cover the use of all forms of expressed RNAi in humans, including shRNA

siRNA (small interfering RNA), is an intermediate in the RNA interference (RNAi) pathway. It occurs naturally in the cytoplasm or may be synthesized externally and introduced to the cell.

shRNA (short hairpin RNA) is the most widely used form of ddRNAi. shRNA is produced inside the target cell from a DNA construct that has been delivered to the nucleus.

The differences between them are summarized in this table, based on Rao, Vorhies, Senzer et al1 and DiGiusto, Krishnan, Li et al2 and described in more detail below.

Criterion

siRNA

shRNA

Nomenclature

Small Interfering RNA

Short Hairpin RNA

Source

Laboratory synthesis

Nuclear expression

Delivery to the cell

Via synthetic/natural polymers and lipids to the cytoplasm

Via viral and other gene therapy vectors to the nucleus.

Persistence

99% degraded after 48 hours

Expressed for up to 3 years.

Administration

Local or limited systemic injection

Local and systemic injection

Dosage

High (low nM)

Low (5 copies)

Likelihood of specific ‘off target’ effects

Higher than shRNA

Lower than siRNA

Likelihood of non-specific ‘off targets’ effects

Higher immune activation, inflammation and toxicity

Lower immune activation, inflammation and toxicity

Application

Acute disease conditions; Where high doses are tolerable

Chronic, life threatening diseases or disorders; Where low doses are desirable

siRNA

siRNA is formed in the cell from shRNA or from long synthetic dsRNA by the Dicer enzyme, and is later separated into two short strands, one of which binds to the target mRNA and cleaves it, preventing the unwanted protein from being made. The first publication in 1998 by Nobel Prize winners Fire and Mello described RNA interference in worms induced by synthetic long double stranded RNA molecules. Synthetic siRNA was first described by Zamore et al in 2000, and remains the most widely used RNAi modality for gene silencing. In the siRNA approach, specific siRNAs are synthesized in the laboratory to silence specific proteins in target cells which are implicated in disease.

Because siRNA is composed of RNA and is inherently fragile, it is difficult to get into the target cell’s cytoplasm and, once there, is quickly degraded. This means that relatively high doses (in the nanomole range) are needed to achieve the desired level of gene silencing, and that treatment must be ongoing.

shRNA

shRNA is short hairpin RNA, double stranded RNA (dsRNA) which is created in the cell from a DNA construct encoding a sequence of single stranded RNA and its complement, separated by a stuffer fragment, allowing the RNA molecule to fold back on itself, creating a dsRNA molecule with a hairpin loop. (What is ddRNAi). In its synthetic form, shRNA suffers from the same constraints as outlined above for siRNA. However, when it is produced inside the cell from a DNA construct, it has the positive characteristics of siRNA, yet is produced continuously by the target cell’s own machinery.

The target cell can be directed to produce shRNA by specific DNA sequences introduced to the cell via a small gene cassette which travels to the nucleus. Here the introduced DNA either becomes part of the cell’s own DNA or persists in the nucleus, and instructs the cell to produce the specific shRNA, which is then processed by Dicer to siRNA and continues along the RNAi pathway via RISC to silence the gene.

Unlike siRNA, this DNA-directed shRNA mechanism requires a minute dose of DNA (in the range of 5 copies) yet the effect is long-lasting from a single dose. This is the RNAi modality for which Benitec Biopharma holds over 50 global patents.